A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure

Bo Li, Xu Li, Bing Wang, Tao Yan

Research output: Contribution to journalArticlepeer-review

Abstract

The high diversity of bacterial antibiotic resistance genes (ARGs) and the different health risks due to their association with different bacterial hosts require environmental ARG risk assessment to have capabilities of both high throughput and host differentiation. Current whole genome sequencing of cultivated isolates is low in throughput, while direct metagenomic next generation sequencing (mNGS) of environmental samples is nonselective with respect to bacterial hosts. This study introduced a population metagenomic approach that combines isolate library construction and mNGS of the population metagenomic DNA, which enables studying ARGs and their association with mobile genetic elements (MGEs) in a specific bacterial population. The population metagenomic approach was demonstrated with the E. coli population in cattle manure, which detected the co-location of multiple ARGs on the same MGEs and their correspondence to the prevalence of resistance phenotypes of the E. coli isolates. When compared with direct mNGS of the cattle manure samples, the E. coli population metagenomes exhibited a significantly different resistome and an overall higher relative abundance of ARGs and horizontal gene transfer risks.

Original languageEnglish (US)
JournalApplied and environmental microbiology
Volume88
Issue number7
DOIs
StatePublished - Apr 2022

Keywords

  • Escherichia coli
  • antibiotic resistance
  • mobile genetic elements
  • population metagenomic sequencing

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Ecology
  • Applied Microbiology and Biotechnology

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